Building with Intel Compiler on a supercomputer

2022-06-04T13:27:28Z

I want to build Delft3D 62441/ on a supercomputer using Intel. However, no matter what Intel Compiler (2020, 2019, 2018) I'm using, it fails during "make ds-install".

I modified the file build.sh for the Intel usage. Please check the attached files for the file and logs.

The error in make.log (same as in the attached file) is as below.

Making install in esm_create
make[4]: ディレクトリ `/home/usr3/p70133d/delft3d_repo/62441/src/utils_lgpl/esmfsm/tests/esm_create' に入ります
/bin/sh ../../../../libtool --tag=CC --mode=link icc -std=gnu99 -D_GNU_SOURCE -DSTR_LEN_AT_END -DWITH_DELFTONLINE -O2 -o esm_create esm_create.o ../../../../utils_lgpl/esmfsm/packages/esmfsm/src/fsm/libESMFSM.la -ldl -lrt -lexpat -lstdc++
libtool: link: icc -std=gnu99 -D_GNU_SOURCE -DSTR_LEN_AT_END -DWITH_DELFTONLINE -O2 -o esm_create esm_create.o ../../../../utils_lgpl/esmfsm/packages/esmfsm/src/fsm/.libs/libESMFSM.a -ldl -lrt -lexpat -lstdc++
ld: ../../../../utils_lgpl/esmfsm/packages/esmfsm/src/fsm/.libs/libESMFSM.a(esm.o): undefined reference to symbol 'pthread_once@@GLIBC_2.2.5'
//usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line
make[4]: *** [esm_create] エラー 1
make[4]: ディレクトリ `/home/usr3/p70133d/delft3d_repo/62441/src/utils_lgpl/esmfsm/tests/esm_create' から出ます
make[3]: *** [install-recursive] エラー 1
make[3]: ディレクトリ `/home/usr3/p70133d/delft3d_repo/62441/src/utils_lgpl/esmfsm/tests' から出ます
make[2]: *** [install-recursive] エラー 1
make[2]: ディレクトリ `/home/usr3/p70133d/delft3d_repo/62441/src/utils_lgpl/esmfsm' から出ます
make[1]: *** [install-recursive] エラー 1
make[1]: ディレクトリ `/home/usr3/p70133d/delft3d_repo/62441/src/utils_lgpl' から出ます
make: *** [install-recursive] エラー 1

My environment settings in .bashrc is as below.

### Load Intel Compilers
#module load intel/2018.3
module load intel/2019.4
#module load intel/2020.1
#module load oneapi/2021.3

### ~/.bashrc Settings for Intel Compiler
export CC=icc
export CXX=icpc
export CFLAGS="-O2"
export CXXFLAGS="-O2"
export F77=ifort
export FC=ifort
export F90=ifort
export FFLAGS="-O2"
export CPP="icc -E"
export CXXCPP="icpc -E"
export MPIF77=mpiifort
export MPIF90=mpiifort
export MPICXX=mpiicc

### NetCDF in ITO
export NETCDF="/home/app/a/NetCDF-4.4.1.1"
export NETCDF_CFLAGS="/home/app/a/NetCDF-4.4.1.1/include"
export NETCDF_LIBS="/home/app/a/NetCDF-4.4.1.1/lib"
export LD_LIBRARY_PATH="/home/app/a/NetCDF-4.4.1.1/lib:$LD_LIBRARY_PATH"
export PATH="/home/app/a/NetCDF-4.4.1.1/bin:$PATH"
export PKG_CONFIG_PATH_LIBS="home/app/a/NetCDF-4.4.1.1/lib/pkgconfig:$PKG_CONFIG_PATH"

Your helps and hints are the most welcome.